DGRPool

GWAS results were computed on dm3 genome.

If you want to make an independent analysis with DGRP2 or PLINK2, you can find here prepared input files for this phenotype: DGRP2 results PLINK2 results

Full results

Phenotype distribution and association to known covariates

Shapiro-Wilk test of normality (p-value=8.747e^-18)
Null Hypothesis is rejected (p<=0.05).
Interpretation: NOT NORMAL distribution of this phenotype

We tested for association of this phenotype with 6 known covariates Huang et al., 2014 using both ANOVA and Kruskal-Wallis association tests.

ANOVA test
No significant result.

Kruskal-Wallis test
No significant result.

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

11066 significant hits at p-value < 0.001. The 1000 top results are displayed in the table below.

We performed a gene enrichment calculation (Fisher's exact test) of all GWAS-associated genes at p < 0.001. Genesets were taken from two database: the Gene Ontology (GO) and the FlyBase phenotypes. GO enrichment FlyBase phenotype enrichment

Variant impact HIGH MODERATE LOW MODIFIER

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Chromosome	Position	ID	Reference	Variant	p-value	FDR_BH	Transcript annotation	Binding site annotation
2L	1456543	2L_1456543_SNP [dm3] 2L_1456543_SNP [dm6]	G	A	0	0	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
3L	14654911	3L_14654911_DEL [dm3] 3L_14661811_DEL [dm6]	TCTGGATATATT...	T	0	0	INTRON dlp	TF binding site BDTNP1_TFBS_twi
2R	8228977	2R_8228977_SNP [dm3] 2R_12341472_SNP [dm6]	G	T	3.622e^-59	1.375e^-53	INTRON CG8839	TF binding site BDTNP1_TFBS_twi mE1_TFBS_cad
2L	1449022	2L_1449022_SNP [dm3] 2L_1449022_SNP [dm6]	G	A	3.696e^-59	1.375e^-53	INTERGENIC	TF binding site BDTNP1_TFBS_twi
2L	1453514	2L_1453514_SNP [dm3] 2L_1453514_SNP [dm6]	C	T	3.696e^-59	1.375e^-53	INTERGENIC
2L	1452271	2L_1452271_DEL [dm3] 2L_1452271_DEL [dm6]	CTCGCTGC	C	1.708e^-58	5.296e^-53	INTERGENIC	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
3R	27452818	3R_27452818_SNP [dm3] 3R_31627096_SNP [dm6]	C	T	3.306e^-51	8.787e^-46	INTRON kek6
3L	4992706	3L_4992706_SNP [dm3] 3L_4992706_SNP [dm6]	A	T	5.519e^-20	9.334e^-15	INTRON Con
3L	5068314	3L_5068314_SNP [dm3] 3L_5068314_SNP [dm6]	T	G	5.519e^-20	9.334e^-15	INTRON Con
3L	5145219	3L_5145219_SNP [dm3] 3L_5152119_SNP [dm6]	G	A	5.519e^-20	9.334e^-15	UPSTREAM Srp54k INTRON Gen	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_HSA mE1_TFBS_Ubx
X	18131388	X_18131388_SNP [dm3] X_18237355_SNP [dm6]	C	A	5.519e^-20	9.334e^-15	INTERGENIC
3L	3692834	3L_3692834_SNP [dm3] 3L_3692834_SNP [dm6]	G	T	1.010e^-19	1.299e^-14	DOWNSTREAM CR43485 INTERGENIC
3L	3699189	3L_3699189_SNP [dm3] 3L_3699189_SNP [dm6]	G	A	1.010e^-19	1.299e^-14	INTERGENIC
3L	3701232	3L_3701232_SNP [dm3] 3L_3701232_SNP [dm6]	T	G	1.010e^-19	1.299e^-14	INTERGENIC
X	7242672	X_7242672_SNP [dm3] X_7348639_SNP [dm6]	C	A	1.092e^-19	1.299e^-14	INTRON CR44357 & 1 other
3L	4832512	3L_4832512_SNP [dm3] 3L_4832512_SNP [dm6]	G	A	1.117e^-19	1.299e^-14	NON_SYNONYMOUS_CODING CG13708	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
X	8689714	X_8689714_DEL [dm3] X_8795681_DEL [dm6]	CGC	T	1.759e^-19	1.655e^-14	INTRON Lim1
2L	11878165	2L_11878165_SNP [dm3] 2L_11878165_SNP [dm6]	T	G	1.831e^-19	1.655e^-14	UPSTREAM Pde1c INTRON Pde1c
2L	16029815	2L_16029815_SNP [dm3] 2L_16029815_SNP [dm6]	G	A	2.010e^-19	1.655e^-14	INTRON beat-Ic
3L	5244328	3L_5244328_SNP [dm3] 3L_5251228_SNP [dm6]	T	C	2.013e^-19	1.655e^-14	INTRON shep	TF binding site mE1_TFBS_inv
2R	15118029	2R_15118029_SNP [dm3] 2R_19230524_SNP [dm6]	T	C	2.045e^-19	1.655e^-14	INTRON cora	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_z mE1_TFBS_HSA mE1_TFBS_Trl
2L	11878029	2L_11878029_SNP [dm3] 2L_11878029_SNP [dm6]	C	A	2.085e^-19	1.655e^-14	UPSTREAM Pde1c INTRON Pde1c
2L	11878043	2L_11878043_SNP [dm3] 2L_11878043_SNP [dm6]	C	T	2.085e^-19	1.655e^-14	UPSTREAM Pde1c INTRON Pde1c
2L	3237517	2L_3237517_SNP [dm3] 2L_3237517_SNP [dm6]	T	A	2.134e^-19	1.655e^-14	INTERGENIC
2L	15861412	2L_15861412_SNP [dm3] 2L_15861412_SNP [dm6]	A	G	3.786e^-19	2.818e^-14	INTERGENIC
2L	2340566	2L_2340566_SNP [dm3] 2L_2340566_SNP [dm6]	T	A	4.072e^-19	2.914e^-14	SYNONYMOUS_CODING eys INTRON CG9967	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA mE1_TFBS_sens
2R	7963730	2R_7963730_SNP [dm3] 2R_12076225_SNP [dm6]	G	T	7.553e^-19	5.204e^-14	INTRON CG8888
3L	1527025	3L_1527025_SNP [dm3] 3L_1527025_SNP [dm6]	C	T	1.046e^-18	6.951e^-14	INTRON CG12090	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_inv
2R	19687941	2R_19687941_SNP [dm3] 2R_23800418_SNP [dm6]	T	A	1.924e^-18	1.129e^-13	INTERGENIC
2L	10214147	2L_10214147_SNP [dm3] 2L_10214147_SNP [dm6]	C	T	1.969e^-18	1.129e^-13	SYNONYMOUS_CODING Npc1a DOWNSTREAM CG4901	TF binding site mE1_TFBS_h mE1_TFBS_HSA
2R	4911647	2R_4911647_SNP [dm3] 2R_9024142_SNP [dm6]	A	G	1.969e^-18	1.129e^-13	INTRON CG8170	TF binding site BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3R	9533177	3R_9533177_SNP [dm3] 3R_13707455_SNP [dm6]	G	A	1.969e^-18	1.129e^-13	SYNONYMOUS_CODING Adgf-C	TF binding site mE1_TFBS_cad
X	18118363	X_18118363_SNP [dm3] X_18224330_SNP [dm6]	C	T	2.002e^-18	1.129e^-13	INTRON CG33639
3R	11173792	3R_11173792_SNP [dm3] 3R_15348070_SNP [dm6]	C	A	2.607e^-18	1.427e^-13	UTR_5_PRIME CG42726 & 1 other DOWNSTREAM CG31301	TF binding site BDTNP1_TFBS_dl
2L	16966722	2L_16966722_SNP [dm3] 2L_16966722_SNP [dm6]	G	C	3.764e^-18	2.001e^-13	DOWNSTREAM CR45285 INTERGENIC
X	19227973	X_19227973_SNP [dm3] X_19333940_SNP [dm6]	G	A	6.775e^-18	3.409e^-13	INTRON nAChRalpha7
2L	16293998	2L_16293998_DEL [dm3] 2L_16293998_DEL [dm6]	AAACATTTCTTCA...	A	6.779e^-18	3.409e^-13	UPSTREAM CG13258 & 2 others INTERGENIC
2L	16994576	2L_16994576_SNP [dm3] 2L_16994576_SNP [dm6]	G	C	6.980e^-18	3.417e^-13	DOWNSTREAM beat-IIIb INTERGENIC
X	15382956	X_15382956_SNP [dm3] X_15488923_SNP [dm6]	T	A	3.061e^-16	1.460e^-11	UPSTREAM Gmap INTRON Gmap
3L	4944808	3L_4944808_SNP [dm3] 3L_4944808_SNP [dm6]	A	G	7.560e^-16	3.516e^-11	INTRON Con
2R	15117861	2R_15117861_SNP [dm3] 2R_19230356_SNP [dm6]	A	T	8.840e^-16	4.011e^-11	INTRON cora	TF binding site BDTNP1_TFBS_z mE1_TFBS_HSA mE1_TFBS_Trl
X	7237230	X_7237230_DEL [dm3] X_7343197_DEL [dm6]	CTC	C	1.166e^-15	5.166e^-11	DOWNSTREAM CBP INTRON CR44357 & 1 other
2L	20890441	2L_20890441_SNP [dm3] 2L_20890441_SNP [dm6]	C	T	1.264e^-15	5.386e^-11	UPSTREAM sky INTRON sky & 1 other	TF binding site BDTNP1_TFBS_dl mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
3L	4944798	3L_4944798_SNP [dm3] 3L_4944798_SNP [dm6]	G	A	1.274e^-15	5.386e^-11	INTRON Con
3L	3924015	3L_3924015_INS [dm3] 3L_3924015_INS [dm6]	T	TCCAC	1.713e^-15	7.082e^-11	INTRON Eip63F-1
2R	8228957	2R_8228957_SNP [dm3] 2R_12341452_SNP [dm6]	A	T	2.488e^-15	1.006e^-10	INTRON CG8839	TF binding site BDTNP1_TFBS_twi mE1_TFBS_cad
2R	7963722	2R_7963722_SNP [dm3] 2R_12076217_SNP [dm6]	G	C	2.950e^-15	1.168e^-10	INTRON CG8888
X	7238004	X_7238004_SNP [dm3] X_7343971_SNP [dm6]	C	T	3.073e^-15	1.191e^-10	INTRON CR44357 & 1 other
2L	1453855	2L_1453855_SNP [dm3] 2L_1453855_SNP [dm6]	G	A	4.315e^-15	1.626e^-10	INTERGENIC
2L	9299453	2L_9299453_SNP [dm3] 2L_9299453_SNP [dm6]	T	A	4.371e^-15	1.626e^-10	UTR_3_PRIME Ggamma30A
X	18636495	X_18636495_DEL [dm3] X_18742462_DEL [dm6]	TCAGATT	T	8.385e^-15	3.059e^-10	INTERGENIC
2L	10657215	2L_10657215_SNP [dm3] 2L_10657215_SNP [dm6]	A	T	1.972e^-14	7.054e^-10	UPSTREAM CR45692 INTERGENIC
3R	21156154	3R_21156154_SNP [dm3] 3R_25330432_SNP [dm6]	G	A	3.156e^-14	1.065e^-9	SYNONYMOUS_CODING CHKov2 DOWNSTREAM CG10669
3R	21182090	3R_21182090_SNP [dm3] 3R_25356368_SNP [dm6]	G	C	3.156e^-14	1.065e^-9	INTRON Fur1	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3R	21210916	3R_21210916_SNP [dm3] 3R_25385194_SNP [dm6]	T	G	3.156e^-14	1.065e^-9	DOWNSTREAM CG31437 INTRON Fur1
3L	3698221	3L_3698221_SNP [dm3] 3L_3698221_SNP [dm6]	C	T	3.205e^-14	1.065e^-9	INTERGENIC
2R	5408498	2R_5408498_SNP [dm3] 2R_9520993_SNP [dm6]	T	C	5.573e^-14	1.819e^-9	INTRON brp	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
3R	22628288	3R_22628288_SNP [dm3] 3R_26802566_SNP [dm6]	C	T	6.150e^-14	1.973e^-9	INTRON Tl	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3R	14486518	3R_14486518_SNP [dm3] 3R_18660796_SNP [dm6]	A	C	1.475e^-13	4.651e^-9	SYNONYMOUS_CODING CstF-64 DOWNSTREAM Cpsf73	TF binding site BDTNP1_TFBS_sna mE1_TFBS_cad mE1_TFBS_chinmo
2R	16055276	2R_16055276_SNP [dm3] 2R_20167771_SNP [dm6]	G	A	2.331e^-13	7.229e^-9	INTERGENIC
3L	12950264	3L_12950264_SNP [dm3] 3L_12957164_SNP [dm6]	G	C	2.513e^-13	7.540e^-9	INTERGENIC
3L	12950269	3L_12950269_SNP [dm3] 3L_12957169_SNP [dm6]	A	T	2.513e^-13	7.540e^-9	INTERGENIC
3L	17559710	3L_17559710_DEL [dm3] 3L_17566610_DEL [dm6]	CAC	C	4.040e^-13	1.193e^-8	UPSTREAM snoRNA:Me28S-A576 INTRON Eip74EF	TF binding site mE1_TFBS_cad mE1_TFBS_HSA
2L	1467775	2L_1467775_SNP [dm3] 2L_1467775_SNP [dm6]	C	T	4.165e^-13	1.211e^-8	INTERGENIC
2R	2968730	2R_2968730_SNP [dm3] 2R_7081225_SNP [dm6]	A	T	6.244e^-13	1.787e^-8	INTERGENIC	TF binding site BDTNP1_TFBS_twi
X	7237259	X_7237259_SNP [dm3] X_7343226_SNP [dm6]	T	G	1.321e^-12	3.724e^-8	DOWNSTREAM CBP INTRON CR44357 & 1 other
2L	1468114	2L_1468114_SNP [dm3] 2L_1468114_SNP [dm6]	G	A	1.807e^-12	5.019e^-8	INTERGENIC
2L	1468712	2L_1468712_SNP [dm3] 2L_1468712_SNP [dm6]	T	C	2.435e^-12	6.663e^-8	INTERGENIC	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
2R	16055254	2R_16055254_INS [dm3] 2R_20167749_INS [dm6]	A	ACTTGCA	2.611e^-12	7.039e^-8	INTERGENIC
2L	7804639	2L_7804639_SNP [dm3] 2L_7804639_SNP [dm6]	A	G	3.162e^-12	8.404e^-8	SYNONYMOUS_CODING cdc14
2R	12443258	2R_12443258_SNP [dm3] 2R_16555753_SNP [dm6]	G	C	3.680e^-12	9.130e^-8	NON_SYNONYMOUS_CODING Syn2
2R	12443321	2R_12443321_SNP [dm3] 2R_16555816_SNP [dm6]	C	T	3.680e^-12	9.130e^-8	INTRON Syn2
2R	6745762	2R_6745762_SNP [dm3] 2R_10858257_SNP [dm6]	C	A	3.680e^-12	9.130e^-8	INTRON CG30015	TF binding site mE1_TFBS_HSA mE1_TFBS_sens
3L	7861204	3L_7861204_SNP [dm3] 3L_7868104_SNP [dm6]	C	G	3.680e^-12	9.130e^-8	UPSTREAM Pdp1 & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl
X	18121513	X_18121513_SNP [dm3] X_18227480_SNP [dm6]	T	A	3.680e^-12	9.130e^-8	EXON CR45622
2R	12443332	2R_12443332_SNP [dm3] 2R_16555827_SNP [dm6]	C	A	5.431e^-12	1.329e^-7	INTRON Syn2
X	3770074	X_3770074_SNP [dm3] X_3876041_SNP [dm6]	C	A	5.756e^-12	1.373e^-7	NON_SYNONYMOUS_CODING CG2930
X	3770137	X_3770137_SNP [dm3] X_3876104_SNP [dm6]	G	A	5.756e^-12	1.373e^-7	SYNONYMOUS_CODING CG2930
3L	4936033	3L_4936033_SNP [dm3] 3L_4936033_SNP [dm6]	C	T	6.174e^-12	1.436e^-7	DOWNSTREAM Con INTERGENIC	TF binding site BDTNP1_TFBS_twi
3L	4936043	3L_4936043_SNP [dm3] 3L_4936043_SNP [dm6]	T	A	6.174e^-12	1.436e^-7	DOWNSTREAM Con INTERGENIC	TF binding site BDTNP1_TFBS_twi
2L	19075104	2L_19075104_SNP [dm3] 2L_19075104_SNP [dm6]	C	T	7.946e^-12	1.793e^-7	UPSTREAM CG17572 EXON CR33315	TF binding site BDTNP1_TFBS_twi
2R	8013966	2R_8013966_SNP [dm3] 2R_12126461_SNP [dm6]	C	T	8.076e^-12	1.793e^-7	INTERGENIC	TF binding site mE1_TFBS_eve mE1_TFBS_HSA
2L	1456943	2L_1456943_SNP [dm3] 2L_1456943_SNP [dm6]	A	T	8.095e^-12	1.793e^-7	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	1461380	2L_1461380_SNP [dm3] 2L_1461380_SNP [dm6]	T	C	8.095e^-12	1.793e^-7	INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cnc mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_sens
X	10350967	X_10350967_SNP [dm3] X_10456934_SNP [dm6]	A	G	9.169e^-12	2.007e^-7	INTERGENIC
2R	19687660	2R_19687660_SNP [dm3] 2R_23800137_SNP [dm6]	T	A	1.162e^-11	2.515e^-7	INTERGENIC
2L	7804374	2L_7804374_SNP [dm3] 2L_7804374_SNP [dm6]	C	G	1.210e^-11	2.588e^-7	UTR_3_PRIME cdc14 INTRON cdc14
2L	3450168	2L_3450168_SNP [dm3] 2L_3450168_SNP [dm6]	T	G	1.311e^-11	2.773e^-7	INTRON Snx1	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2L	3316078	2L_3316078_SNP [dm3] 2L_3316078_SNP [dm6]	G	T	1.429e^-11	2.987e^-7	SYNONYMOUS_CODING CG3277 DOWNSTREAM CG3326
X	14849280	X_14849280_SNP [dm3] X_14955247_SNP [dm6]	T	A	1.654e^-11	3.381e^-7	UPSTREAM eag & 1 other INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_bab1 mE1_TFBS_h mE1_TFBS_HSA mE1_TFBS_sens
X	15390230	X_15390230_SNP [dm3] X_15496197_SNP [dm6]	G	C	1.654e^-11	3.381e^-7	INTRON Gmap	TF binding site BDTNP1_TFBS_dl
3R	24756336	3R_24756336_SNP [dm3] 3R_28930614_SNP [dm6]	T	C	2.325e^-11	4.579e^-7	INTRON CG14521
3R	26096374	3R_26096374_SNP [dm3] 3R_30270652_SNP [dm6]	A	T	2.363e^-11	4.579e^-7	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_hkb mE1_TFBS_HSA mE1_TFBS_Trl
3R	26097564	3R_26097564_SNP [dm3] 3R_30271842_SNP [dm6]	G	C	2.363e^-11	4.579e^-7	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_Trl
3R	26097576	3R_26097576_SNP [dm3] 3R_30271854_SNP [dm6]	A	T	2.363e^-11	4.579e^-7	INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_Trl
3R	26098638	3R_26098638_SNP [dm3] 3R_30272916_SNP [dm6]	C	T	2.363e^-11	4.579e^-7	INTERGENIC	silencer mE1_HDAC_PRE TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_inv mE1_TFBS_Trl
3L	4754555	3L_4754555_SNP [dm3] 3L_4754555_SNP [dm6]	T	C	2.544e^-11	4.880e^-7	UPSTREAM CG12493 INTRON RhoGEF64C
2R	9392955	2R_9392955_SNP [dm3] 2R_13505450_SNP [dm6]	C	T	2.628e^-11	4.989e^-7	SYNONYMOUS_CODING mars UPSTREAM mip120	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3R	22628866	3R_22628866_SNP [dm3] 3R_26803144_SNP [dm6]	C	T	3.353e^-11	6.238e^-7	INTRON Tl	TF binding site mE1_TFBS_sens
3R	22628876	3R_22628876_SNP [dm3] 3R_26803154_SNP [dm6]	G	T	3.353e^-11	6.238e^-7	INTRON Tl	TF binding site mE1_TFBS_sens

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By genomic position
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Microbiota_OTU034 phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results